When software applications are installed onto a computing device, ancillary files are often installed in addition to the executable application file. These ancillary files may reside in different directory locations from the application itself. When the application is later uninstalled, the ancillary files may not be removed, which may consume storage resources. In addition, the ancillary files may be used by more than one application. If the user removes the ancillary files manually, performance of the other applications may be affected. Accordingly, there may be a need for an improved apparatus and methods for uninstalling applications more thoroughly without negatively impacting application performance.